Normalizes (and transforms) ChIP-seq read coverage

Normalizes the ChIP-seq read counts by scaling to the reference ChIP-seq library size, and transforms the ChIP-seq read counts.

normalize_chip(
  chip_counts,
  idxstats_file,
  ref_size = 2e+07,
  transform = c("none", "asinh", "log2", "sqrt")
)

Arguments

chip_counts

A vector of ChIP-seq counts.

idxstats_file

The idxstats file generated by samtools.

ref_size

ChIP-Seq reference library size (Default: 20 million).

transform

Type of transformation for the ChIP read counts. Options are ‘none’ (no transformation), ‘asinh’, ‘log2’, and ‘'sqrt'’.

Value

A vector of transformed ChIP-seq counts.